evil homer, with my version of After Effects it does the same thing.
in my experience i think After Effects is more designed for Graphics, Titles, Special Effects etc, rather than putting a whole production together.
I myself, always make the compositions in After Effects then import them into Premier Pro to add the sound track, sound effects etc.
If the file already has an attached audio to it, i completely disregard it in After Effects then add the same songs etc into Premier pro and edit the soundtrack there
After Effects isn't really made for editing full productions